Proteome Software Newsletter

Welcome to the Proteome Software Newsletter!

Influence and prioritize our development efforts by filling out this
survey. We need your input.

New and improved proteomics reference collection. Check out the Proteome Software Web Library.This wiki is under construction.

Download iProteome from the Apple App Store by searching on your device.

Bug Fixes and Release Notes for Scaffold 3.6

Scaffold Software Suite Brochure

Proteome Software News...

Hint of the day:Queue Structured Directories for Loading. Save time and make your life easier by letting Scaffold load and organize your complex proteomics experiments. Create a directory structure that includes a folder for a category and subfolders for biosamples, each with MS/MS sample files inside. Then, create an experiment in Scaffold, go to Experiment > Queue Structured Directories for Loading and let Scaffold take care of the rest.

>>> Release Notes

Scaffold 3.6.3 has been released.
Evaluate for 14 days here...

The current version of Scaffold 3.6.3 builds on the improvements made with the release of Scaffold 3.5 in May, where we’ve added several key features including quantitation based on precursor ion intensity (for data from Proteome Discoverer, Mascot Distiller and Spectrum Mill). Additionally automatic parsing of FASTA files will support flexible matching of accession numbers to databases. Other improvements have been made in handling FDR, TIC and retention time.

To learn more...

Scaffold Q+ and Q+S

Scaffold Q+ already works to push the boundaries of multiplexed quantitative data analysis, including SILAC support with
Scaffold Q+S. The process of normalization is key in this analysis. For more details, check out Brian’s ASMS presentation “Advancing Statistical Analysis of Multiplexed MS/MS Quantitative Data with Scaffold Q+”

Read more...

Scaffold PTM 2.0

Search engines are really good at telling you if a peptide is phosphorylated, but not at telling you where that phosphorylation is. That’s where Scaffold PTM enters. It’s designed to re-interpret all of the modifications (not just phosphorylation) in your data sets and give you a confidence level for which sites are modified.

Learn more about Scaffold PTM...

Proteome Software is Distributing Matrix Science's Mascot Distiller

Mascot Distiller, a powerful proteomics workflow application is now being distributed by Proteome Software. Contact us to get your free 30 day key.

For more information...

Proteome Software and Agilent Technologies Partnership

Agilent Technologies develops and supports Spectrum Mill software, for searching and analyzing MS/MS proteomics experiments. We support the result files from Spectrum Mill in Scaffold and have built a partnership to make this compatibility more robust.

In other news. . .

Scaffold 4.0 is under development. While we can't confirm all
of the new features, it will include MaxQuant label-free support,
enhancements to Gene Ontology (GO Term) filtering, as well as an export
interface for PRIDE.

Check out our
Product Feature Table to see which search-engines and file-types are supported. This table also compares quantitation methods, differential expression metrics, filtering, and visualization tools within the Scaffold Software Suite.

Reminder: as an application that uses the Java Virtual Machine (JVM), Scaffold relies heavily on memory to process results and hold those results for immediate manipulation and visualization. This is why it is very important to remember to allocate your memory in the Preferences section under Edit in Scaffold.